Layers

ImFusion Labels supports multiple layers of the same annotation type. Instead of having a one-to-one association between a dataset and a type of annotation, there can be multiple sets of annotations associated to each dataset. Each layer is individually defined with its own labels, and only a single layer is active at a time. This is useful for example for segmenting overlapping structures, or for having different sets of annotations for different annotators.

Defining layers

Defining the layers of a project is done in the settings, by activating the Expert feature level. Two tables are then shown on the right-hand side: the top one is used to define how many layers there are, and the bottom one is used to define the content of the currently selected layer.

In the above example, three pixelwise segmentations layers are defined, the first one is selected.

The labels of each layer are completely independent.

Changing layers

If a project has been defined with multiple layers, a button to switch the active layers is shown:

• In the database view, in the top right of the window.

• In the display options of the annotation view, at the bottom of the side bar.

When the button is clicked, it shows a drop-down with the list of all layers, which can then be clicked to change the active layers. In this example, the project only contains pixelwise segmentation. It has two layers, one named ‘Lungs’ and the other ‘Lesions’.

As the active layer is changed, the thumbnail of each dataset is updated to show the annotation corresponding to the newly selected layer. If a dataset is currently loaded, the annotation is also switched to correspond to the active layers. Note that the previously active annotation is automatically saved.

Additionally, the Active Label table present in various tools (such as the Brush) displays all layers of the Project as a single table. The labels of each layer are grouped under a collapsible header showing the name of the layer. The currently active layer and its labels are painted in full opacity, while other layers are painted in semi-transparent. The table allows selecting labels in the active layer and switching between layers.

Exporting with layers

When exporting data of a project with layers, the layer to be exported must be selected in the Label Encoding section. At the moment, only one layer can be exported at a time, but this may change in the future.

Note

One notable use-case for this feature is pixelwise segmentation of overlapping features. Within one layer, only a single label can be assigned to one pixel, but with multiple layers the overlapping features can be annotated. For example, if one wanted to segment lungs and lesions in a chest CT-scan, one possibility would be to define two layers: the first representing the entire lung, and the second layer representing the lesions, which are a subset of the lungs.